AN incident last June, a few days before Egypt's Islamist President Mohammed Mursi was ousted by the military, made Ahmed realise there had been a significant shift in the country's political atmosphere.

A secular activist in Egypt's revolution that emerged from the Arab Spring uprisings, Ahmed had always staunchly opposed both the security forces and the Muslim Brotherhood.

But that day last June, as he chanted revolutionary slogans and vented his anger outside a police station in the city of Alexandria, a group of bystanders closed round him, demanding to know what he thought he was doing. Ahmed backed down and fled.

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Now he is glad that the Muslim Brotherhood-affiliated Mursi has been ousted from power, but is concerned about the resurgence of the military, security services and police, and the widespread support they enjoy. In the current climate, he thinks: "It is best to keep my mouth shut."

Secular protesters like Ahmed launched and drove the 2011 uprising that toppled the autocratic President Hosni Mubarak. Yet, nearly three years on, many secular activists argue that the threat to human rights from the current regime is even greater than it was under Mubarak. They feel crushed in the battle between the widely supported military and the significant section of society that identifies itself as Islamist.

Today, the police and military feel empowered by the huge demonstrations against Mursi that led to his ousting on July 3. In the weeks that followed, Egypt experienced the worst civil violence in its modern history as the authorities launched a ferocious crackdown on the Muslim Brotherhood.

Hundreds of Brotherhood leaders and supporters have been arrested. Recently, the authorities designated the Brotherhood a terrorist organisation, drastically upping in severity the level of punishment for its members. For its part, the Brotherhood has tried to respond. Over the last few days alone 11 people have been killed in clashes between police and Brotherhood activists in the capital Cairo and the cities of Alexandria, Fayoum and Ismailia.

Since Mursi's ousting, secular activists have largely been absent from these street protests, therefore escaping the attention of the authorities. In recent weeks, however, the authorities have widened their crackdown to include secularists, liberals and leftists. The military-backed interim government recently passed draconian legislation, which Human Rights Watch claims "effectively bans protest".

The police have violently broken up peaceful demonstrations by secularists against these measures, beating and arresting scores of activists. Well-known secular activists have been arrested and referred to trial for allegedly organising illegal protests. A total of 25 people are to face criminal charges for their part in a protest at the Shura Council on November 26. On December 18, the police stormed the offices of the Egyptian Centre for Economic and Social Rights, detaining and beating members of staff and destroying and confiscating equipment.

In addition to a blanket demonisation of Muslim Brotherhood supporters as terrorists, much of the Egyptian media has also launched a campaign of vilification against the secular activists who oppose both the Brotherhood and the military. Revolutionary groups have been labelled as traitors, and the authorities have claimed they are threatening the security of the state and are receiving foreign backing from Israel or America.

According to Amal Sharaf, foreign spokeswoman for the prominent secular activist group April 6 Movement, the result has been that "people now hate us, they are totally brainwashed. Ordinary people insult us and beat us in the street."

Sherif Azer, a human rights activist with Front Line Defenders and the Egyptian Organisation for Human Rights, says his work is more difficult than ever.

"Now what we are really facing is the Egyptian people themselves, the majority of the population, not just the regime - which is much worse than before the revolution," he insists. "When the people you are fighting for call you a traitor and want you to shut up, this definitely affects my daily work."

Many secular activists fear that if the authorities subject them to a crackdown with the same degree of ferocity that has been applied to the Muslim Brotherhood, their groups will be crushed for several years to come. Some have argued that the current climate of repression by the authorities and the level of public hostility means that they should lie low and bide their time, until the situation becomes more favourable.

"I think it's exactly the wrong tactic" argues Omar Robert Hamilton, a film-maker, journalist and member of activist film-making collective Mosireen.

"This is the key point at which people need to stand up, make a noise and be counted on the street because the police think that they can get away with whatever they want and they've been given a free hand by [General] Sisi."

The widespread appeal of Egypt's Defence Minister General Sisi - who announced Mursi's ousting - partly lies in a desire for a "strongman" ruler in the mould of Egypt's second president, Gamal Abdel Nasser Hussein, who led the country from 1956 until his death in 1970.

These days Egypt's economy has plummeted since the uprising that toppled Mubarak broke out on January 25, 2011, and many Egyptians support the crackdown on dissent because they see it as a means of imposing law and order on Egypt's unruly streets and regaining some kind of economic stability.

Many secular activists say they sympathise with this view but that it is misguided and that a repressive "stability" is an illusion.

"Without proper freedoms, proper democracy or proper rights, there will never be stability," argues human rights activist Sherif Azer. "They think that just suppressing people will lead to a stable state, that's what Mubarak did for years and it didn't work at the end."

Galal Amin, professor of economics at the American University in Cairo and author of Whatever Happened To The Egyptian Revolution, states that the "revolution is in a mess".

Amin argues that the malaise can be attributed to the failure of the uprising's leaders to gain political power.

"Throughout the three years [since the 2011 uprising], those who held power and are still holding it do not really belong to the revolutionary camp," he says.

Fractured and divided as the secular revolutionary movement is, it has nevertheless achieved some clear political gains from the 2011 uprising.

"The revolution gave us so much confidence, even now. We feel disappointed because of our leaders but every year we see a new development in ourselves," says 22-year-old Mostafa Wafa, who has participated in many leftist and liberal activist groups since 2009.

He and others like him argue that the space for civil society has grown and freedom of expression has developed in a way that would have been near impossible in Mubarak's time.

Omar Robert Hamilton agrees it was unthinkable that organisations such as Mosireen - which regularly screens political films and highlights abuses committed by the security forces - would have existed under Mubarak.

"The measure of the revolution has always been in these kinds of initiatives and the ways that communities are organising themselves and people are stepping in to fill the gaps left by the non-existent, corrupt state," Hamilton says.

There is certainly evidence that disruption caused by the revolution has led to the formation of many popular committees in often-neglected areas of Cairo. These grassroots organisations initially performed a security function but have developed to provide local services that the state has failed to deliver, including rubbish collection, repair of utilities, organisation of traffic and distribution of subsidised goods.

Independent trade unions have emerged too since the revolution, offering a harsher critique of government practices than the official syndicates which are largely mouthpieces of the authorities. In Cairo, the cultural and artistic space has flourished since the uprising. Political graffiti and art - virtually unknown during Mubarak's time - continues to exert a powerful resonance.

All of these "gains" will of course be put to the test again in the coming weeks and months. On January14-15, Egyptians will vote on the new draft constitution. If the constitution is passed - which seems likely - then presidential and parliamentary elections will follow later in the year.

January also sees the latest instalment of the trial of former President Mursi, on charges of incitement to violence and murder. With the third anniversary of the uprising looming this month there will also be an escalation in protests that will inevitably pose testing questions about the strength of the various actors in Egyptian politics and the nature of the coming political system.

For now, the security forces have the weight of public opinion behind them, but such support can quickly wither, especially if, as many activists believe, the authorities continue to be more concerned with projecting power and protecting their privileges, rather than addressing Egypt's underlying economic and political problems.

The recent laws restricting protests would be futile in the face of the sheer weight of numbers that have toppled previous regimes.

"In February 2011 we all thought that we had achieved this beautiful, miraculous thing and that people would behave in a suitable way going forward. But that was us being young and stupid," admits Omar Robert Hamilton. Hamilton maintains that in perhaps as little as a year or so from now, secular activists could again be galvanised and the revolutionary cause would gain proper momentum.

It is either that, he says, "or it could all be over and everyone is in jail, silent or dead".